Hi @michaelosMCESC,

Unfortunately, if the courses have to be in the same account/subaccount, there is no way to differentiate the themes.  If you have the ability to create new subaccounts, you could create a new one under the current subaccount, move the course into it and apply a different theme there.  This may not work depending on how your school has integrations configured (especially to/from your student information system).

I hope this answer makes sense and helps you out!

-Chris